Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research by Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss, Jean Paul Delgado

“…Abstract Background Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. …”
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Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. by Antonio Garcia-España, Roso Mares, Tung-Tien Sun, Rob Desalle

“…The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life.We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. …”
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Phylogeny of Anoxygenic Photosynthesis Based on Sequences of Photosynthetic Reaction Center Proteins and a Key Enzyme in Bacteriochlorophyll Biosynthesis, the Chlorophyllide Reduct... by Johannes F. Imhoff, Tanja Rahn, Sven Künzel, Sven C. Neulinger

“…Photosynthesis is a key process for the establishment and maintenance of life on earth, and it is manifested in several major lineages of the prokaryote tree of life. The evolution of photosynthesis in anoxygenic photosynthetic bacteria is of major interest as these have the most ancient roots of photosynthetic systems. …”
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Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota) by Todd J. Widhelm, Felix Grewe, Jen-Pan Huang, Joel A. Mercado-Díaz, Bernard Goffinet, Robert Lücking, Bibiana Moncada, Roberta Mason-Gamer, H. Thorsten Lumbsch

“…Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.…”
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Evolutionary patterns of diadromy in fishes: more than a transitional state between marine and freshwater by Joel B. Corush

“…Abstract Background Across the tree of life there are numerous evolutionary transitions between different habitats (i.e., aquatic and terrestrial or marine and freshwater). …”
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Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences by Matthew A. Campbell, Michael E. Alfaro, Max Belasco, J. Andrés López

“…Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. …”
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Mammals from ‘down under’: a multi-gene species-level phylogeny of marsupial mammals (Mammalia, Metatheria) by Laura J. May-Collado, C. William Kilpatrick, Ingi Agnarsson

“…Although the group has been the subject of decades of phylogenetic research, the marsupial tree of life remains controversial, with most studies focusing on only a fraction of the species diversity within the infraclass. …”
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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources by Bin Ma, Caiyu Lu, Yiling Wang, Jingwen Yu, Kankan Zhao, Ran Xue, Hao Ren, Xiaofei Lv, Ronghui Pan, Jiabao Zhang, Yongguan Zhu, Jianming Xu

“…We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome’s functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. …”
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Transmitting silks of maize have a complex and dynamic microbiome by Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles R. Shearer, Victor Limay-Rios, Lana M. Reid, Manish N. Raizada

“…MiSeq 16S rRNA gene sequencing of 328 open-pollinated silk samples (healthy/Fg-infected) revealed that the TSM contains > 5000 taxa spanning the prokaryotic tree of life (47 phyla/1300 genera), including nitrogen-fixers. …”
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Phytochemical screening, antimalarial activities, and genetic relationship of 16 indigenous Thai Asteraceae medicinal plants: A combinatorial approach using phylogeny and ethnobota... by Desy Liana, Kanchana Rungsihirunrat

“…Interactive phylogenetic tree was generated by Interactive Tree of Life (ITOL, https://itol.embl.de) and showed strong clustered pattern on Asteraceae. …”
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Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram by Michał Burdukiewicz, Katarzyna Sidorczuk, Dominik Rafacz, Filip Pietluch, Jarosław Chilimoniuk, Stefan Rödiger, Przemysław Gagat

“…Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. …”
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The Application of Quantitative Metabolomics for the Taxonomic Differentiation of Birds by Ekaterina A. Zelentsova, Lyudmila V. Yanshole, Yuri P. Tsentalovich, Kirill A. Sharshov, Vadim V. Yanshole

“…A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life.…”
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Darwintree: A Molecular Data Analysis and Application Environment for Phylogenetic Study by Zhen Meng, Hui Dong, Jianhui Li, Zhiduan Chen, Yuanchun Zhou, Xuezhi Wang, Shouzhou Zhang

“…DarwinTree (http://www.darwintree.cn) provides an integrated bioinformatics platform that supports all phases of the analytical pathway for phylogenetic study from data collections, phylogenetic tree constructions, visualization of the tree of life, and web-based rendering to specific application services & data mining. …”
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Assessing the Severity of Traumatic Brain Injury—Time for a Change? by Olli Tenovuo, Ramon Diaz-Arrastia, Lee E. Goldstein, David J. Sharp, Joukje van der Naalt, Nathan D. Zasler

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Evidence for reproductive senescence across ray-finned fishes: A review by Milan Vrtílek, Jakub Žák, Jakub Žák, Martin Reichard, Martin Reichard, Martin Reichard

“…The origin, incidence, and consequences of reproductive senescence vary greatly across the tree of life. In vertebrates, research on reproductive senescence has been mainly focused on mammals and birds, demonstrating that its variation is largely linked to critical life history traits, such as growth patterns, juvenile, and adult mortality, and reproductive strategy. …”
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The Quiet and Underappreciated Rise of Drug-Resistant Invasive Fungal Pathogens by Amir Arastehfar, Cornelia Lass-Flörl, Rocio Garcia-Rubio, Farnaz Daneshnia, Macit Ilkit, Teun Boekhout, Toni Gabaldon, David S. Perlin

“…In this review, we attempt to summarize the burden of antifungal resistance for selected non-<i>albicans</i><i>Candida</i> and clinically important <i>Aspergillus</i> species together with their phylogenetic placement on the tree of life. Moreover, we highlight the different molecular mechanisms between antifungal tolerance and resistance, and comprehensively discuss the molecular mechanisms of antifungal resistance in a species level.…”
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Estimating transcriptome complexities across eukaryotes by James E. Titus-McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers

“…These analyses represent a step toward whole-transcriptome analysis in the emerging field of non-model evolutionary genomics, with key insights for evolutionary inference of complexity changes on deep timescales across the tree of life. We suggest a means to quantify biases generated in ortholog calling and correct complexity analysis for lineage-specific effects. …”
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The relations of St. Bonaventure’s theology of the cross with the Carmelite mysticism. In the realm of Franciscan and Carmelite artistic affinity exemplified by the chosen works of... by Urszula Mazurczak

“…In the present paper the mainstream of Franciscan piety has been pointed out and its relation with the contemplation of the Cross as The Tree of Life, the form of which was assimilated by importing ampoules for the holy oil or other votive items from Palestine. …”
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FACT: Functional annotation transfer between proteins with similar feature architectures by Koestler Tina, von Haeseler Arndt, Ebersberger Ingo

“…<p>Abstract</p> <p>Background</p> <p>The increasing number of sequenced genomes provides the basis for exploring the genetic and functional diversity within the tree of life. Only a tiny fraction of the encoded proteins undergoes a thorough experimental characterization. …”
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Expanding adverse outcome pathways towards one health models for nanosafety by Laura Aliisa Saarimäki, Laura Aliisa Saarimäki, Giusy del Giudice, Giusy del Giudice, Dario Greco, Dario Greco, Dario Greco

“…We anticipate that this new direction of toxicogenomics can support the development of One Health models applicable to groups of chemicals and to multiple species in the tree of life.…”
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